C383 Exam 1Fall 2016

Name _______________________________________ Seat Number ___________

Student ID ____________________________________ Circle your section: M T W R

The last page of this exam contains equations, constants, pKa values, and other information you might find useful.The exam consists of 34 questions worth 100 points plus 8 bonus points on a total of 11 pages. It will be scored out of 100 points.

1-15 _________/30 multiple choice

16-30 _________/30 fill in the blank

31 ________/10

32 ________/10

33. ________/10

34. ________/10

Bonus ________/8

Total:

Regrading: All requests for regrades must be submitted in writing within 48 hours of the return of the exam. You must explicitly state what has been misgraded and why it is an error. The entire exam will be regraded, which could result in points being added or deducted overall.

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Section 1: Multiple Choice. 15 questions, 2 points each.

1. _______The least polar of the major classes of biomolecules is

A) carbohydrates B) nucleic acidsC) proteinsD) lipidsE) none of the above.

2. ________ The amide group of the dipeptide Val-Pro can serve as aA) hydrogen bond donorB) hydrogen bond acceptorC) both hydrogen bond donor and acceptorD) neither hydrogen bond donor nor acceptor

3. _______ The process of nonpolar molecules spontaneously assembling in an aqueous environment can best be explained thermodynamically byA) the negative S of process.B) the negative G of the process.C) the positive H of the process.D) the maximization of van der Waals forces.E) None of the above

4. _________ What is the pH of a 0.1 M succinate/succinic acid buffer?A) 3.2B) 4.2C) 4.9D) 5.6E) cannot be determined from this information

5. _______ The amino acid methionine best fits into the ___________ class of amino acids.

A) polarB) hydrophobicC) positively chargedD) negatively chargedE) zwitterionic

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6. ______ Base stacking contributes to the stability of the double helix by A) The hydrophobic effect. D) Both A and B B) Maximizing van der Waals interactions E) A, B, and CC) Hydrogen bonding

7. ________ All of these statements are true of the DNA denaturation curve except

A) It is sigmoidally shaped.B) It can be used to determine the melting point of a DNA double helix. C) It is measured by absorbance of light by nucleobases as a function of concentration of DNA added.D) It is affected by the relative percent of GC base pairs in the DNA.

8. _________ An alpha helix with a sequence of AWLIIMFAWV is likely to be found A) In the protein core.B) On the protein surface.C) In a disordered loop.D) In the active siteE) In a zinc finger.

9. _______ Anfinsen’s experiment in which he treated RNase A with urea and mercatoethanol and then dialyzed it supports the principle that

A) Replication is semiconservative. B) Protein folding is directed by way of a folding funnel .C) Misfolded proteins can lead to various pathologies such as Alzheimer’s disease.D) The information needed for protein folding is found in the primary sequence.

E) Some proteins are metamorphic and can exist in an equilibrium ensemble of energetically similar folds.

10. _______ Which disease/syndrome is not matched with its biochemical cause?A) Scurvy: lack of a vitamin necessary to maintain collagen structure B) Kwashiorkor: insufficient protein intakeC) Parkinson’s disease: amyloid fibers form from misfolded proteinD) All of the above are properly matched.E) None of the above are properly matched.

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11. _______ Which reaction will occur fastest under enzyme catalyzed conditions? Refer to the table below.

Reaction Uncatalyzed rate (s-) Catalyzed rate (s-) Rate enhancementA B 2.8 x 10-16 39 1.4 x 10 17

C D 1.7 x 10-7 66,000 3.9 x 1011

E F 2.6 x 10-5 50 1.9 x 106

A) A BB) C DC) E FD) They will all proceed equally fast because they are all enzyme catalyzed.E) Cannot be determined from these data.

12. _______ A reaction, which has a negative Go’, starts under conditions in which the ratio of product to reactants is less than one. What is true for the reaction starting under these conditions?

A) It is spontaneous. B) It is nonspontaneous.C) It can be either spontaneous or not spontaneous.D) It is at equilibrium.E) Cannot be determined from this information.

13. _______ The binding energy of the enzyme is maximized when it binds to the

A) substrate.B) cofactor.C) transition state.D) product.E) active site.

14. _______ What is the major conjugate base component of the blood buffer?

A) HPO4-2

B) H2PO4-1

C) HCO3-1

D) CO2

E) H2CO3

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15. _______ Proteases and nucleases are similar in all of these ways except:

A) Both are enzymes. B) Both act on polymeric substrates.C) Both catalyze hydrolysis reactions.D) Both cleave amide bonds.E) Both have active sites.

Section 2: Fill in the blank. 15 questions 2 pointe each

16. According to the Henerson-Hasselbalch equation, the pH of a solution is related to the _______ of the acid and the ratio of the ________________ of the acid and its conjugate base.

17. The net charge of arginine at pH 9.0 is approximately _____________.

18. __________________ and _________________ are two amino acids with amide sidechains.

19. If a -sandwich motif is found on the surface of a protein, it must be ___________________________ so that one face can interact with the water favorably while the other face forms favorable interactions with the core of the protein.

20. _____________________ is a nucleobase found in RNA but not DNA.

21. A _________________ is a compact, independently folded unit of a larger protein.

22. The cyclic DNA of bacteria is underwound so that it can replicate, but it is stabilized by ________________________________.

23. A hairpin turn is likely to contain the amino acids _______________ and _________________ to facilitate the tight turn between two secondary structures.

24. There are two major types of electrophoresis. In SDS-PAGE, proteins are separated on the basis of ___________________________. In isoelectric focusing, proteins are separated on the basis of ___________________.

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25. The __________________________ of a protein sample reflects its purity because it is a measure of the sample’s activity relative to how much protein is in the sample.

26. In gel-filtration chromatography, proteins are separated on the basis of ______________________, with ______________ proteins coming off of the column first.

27. The technique called the Edman Degradation can be used to sequence polypeptides by identifying the amino acid at the _______________________ end of the peptide.

28. The _________________________ model of enzyme/substrate binding is inadequate because the molecules are not static; substrate binding causes an induced fit.

29. An enzyme can increase the rate of reaction by changing the ________________________, but it cannot change the thermodynamics of the reaction.

30. Many enzymes require _______________________ such as Zn+2 or NADH to be active.

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Section 3. Problems. 4 questions 10 points each.

31. The RNA/DNA hybrid pdApU was synthesized. Draw its structure below and indicate the 3’ end, a phosphodiester bond, and one potential hydrogen bond donor group on a nucleobase.

If the similar dinucleotide pUpdA were synthesized, would you expect it to be more or less stable at pH 7? Explain.

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32. A. Draw a titration curve for the amino acid tyrosine. (See the last page for pKa values.)

B. Draw the structure of tyrosine in its predominant ionization state at pH 7.4. Mark this point on the curve you drew in part A.

C. Draw the structure of tyrosine at its isoelectric point Mark this point on the curve you drew in part A.

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33. The isomerization of dihydroxyacetone phosphate (DHAP) to glyceraldehyde 3-phosphate (GAP) has an equilibrium constant of 0.0475 under standard conditions. In the cell, the [DHAP] is 2 x 10-4 M and [GAP] is 3 x 10-6

M.

A. What is the standard free energy for this reaction?

B. Is this reaction spontaneous or nonspontaneous under standard conditions?

C. Is this reaction spontaneous or nonspontaneous under cellular conditions? Show all your work in determining this answer.

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34. Given the name of the enzyme or the reaction it catalyzes, predict the class to which the enzyme belongs: oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase. Fill in the enzyme classes in the blanks below:

A. _____________________ B. ____________________ C. _____________________

D. _____________________ E. ____________________ F. _____________________

G. _____________________ H. ____________________ I. _____________________

J. ______________________

A. phosphoglycerate mutase B. Glyceraldehylde-3-phosphate dehydrogenaseC. Protein tyrosine kinase D. Gutamine synthetase

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Bonus: Draw the structure of the hexapeptide in its major ionization state at pH 10 consistent with the following sequencing data. When the sequence is not known, a comma separates the amino acids.

Amino acid composition: (2R, A, S, V, Y)Amino-terminal analysis: ATrypsin digest: (R,A, V) and (R,S,Y)Carboxypeptidase A digestion: no digestionChymotrypsin digest: (A, R, V, Y) amd (R, S)

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Useful Information:

G0’ = -RT ln Keq R = 8.314 J/mol.K

Amino acid pKa valuesC-terminal 2.2 N-terminal 9.0Aspartate, glutamate 4.1Histidine 6.1Cysteine 8.3Tyrosine 10.9Lysine 10.8Arginine 12.5

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